Genetic and Tabu search algorithms for peptide assembly problem

¹ Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland; J. Błażewicz: jblazewicz@cs.put.poznan.pl
² Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland.

Received: 20 November 2009
Accepted: 5 February 2010

Abstract

Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented. The algorithm has been tested in computational experiment and compared with an existing tabu search method for the same problem. The results clearly show that the genetic algorithm outperformed the tabu search approach.